Recent studies, including the Cryptosporidium parvum Genome Project, have provided evidence for a mitochondrial-derived compartment in this parasite. This organelle appears to lack a genome, and thus must be entirely dependent on nuclear-encoded proteins. Here, we review the evidence for such an organelle in C. parvum and its probable function. There is no adequate treatment for infection by this parasite and so the elucidation of the role of this organelle and the effective targeting of its functions by antimicrobial agents might provide new treatments for infection by C. parvum.